March 03, 2011

Genetic variation in Native Americans consistent with archaeology

The great thing about this study is that the authors came up with a way of studying Native Americans via the genomes of Mexicans. This is possible because Mexican genomes contain largely European and Amerindian segments (and much less African), which can be easily identified as such.

The fact that genomic diversity in Native Americans can be recovered from their admixed descendants presents new hope for prehistoric studies, as in many places of the world (e.g., North Africa or Central Asia), admixture events took place that are not as well understood since they did not happen to be well-recorded by historians.

“In marked contrast to the goals of the Cornell Ancestry Event, which seeks to define ‘diversity’ biologically in terms of universal genetic codes … Indigenous peoples customarily define themselves not biologically, but socio-culturally and politically in terms of varying ideas of nationhood,” the statement says.

... which thus objected to the Genographic Project's sampling of Native Americans.

If researchers can identify Native American DNA in admixed individuals, then there must be something more concrete to being a "Native American" than socio-cultural/political self-definitions.

Moreover, it shows how futile the quest to limit access to Native American DNA for research purposes actually is, because this DNA can be recovered anyway from admixed individuals (such as many Latinos) who don't mind.

Analyses of genetic polymorphism data have the potential to be highly informative about the demographic history of Native American populations, but due to a combination of historical and political factors, there are essentially no autosomal sequence polymorphism data from any Native American group. However, there are many resequencing studies involving Latinos, whose genomes contain segments inherited from their Native American ancestors. In this study, we introduce a new method for estimating local ancestry across the genomes of admixed individuals and show how this method, along with dense genotyping and targeted resequencing, can be used to assay genetic variation in ancestral Native American groups. We analyze roughly 6 Mb of resequencing data from 22 Mexican-Americans to provide the first large-scale view of sequence-level variation in Native Americans. We observe low levels of diversity and high levels of linkage disequilibrium in the Native American-derived sequences, consistent with a recent, severe population bottleneck associated with the initial peopling of the Americas. Using two different computational approaches, one novel, we estimate that this bottleneck occurred roughly 12.5 thousand years ago; when uncertainty in the estimation process is taken into account, our results are consistent with archeological estimates for the colonization of the Americas.

38 comments:

This is another unfortunate attempt by geneticists to turn the origin of Native Americans into a simple computer game. Each lab doesn't bother putting their own findings into a wider context. The authors conclude that Native Americans arrived from Siberia 12,500 years ago as a result of a "severe bottleneck." How can this bottleneck be severe is there're at least 15 distinct mtDNA lineages found in Native Americans? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928495/. For comparison, only 2 mtDNA lineages (M and N) supposedly left Africa.

They also attempt to overturn linguistic evidence for human antiquity in the Americas by saying that "an early occupation of the Americas (> 30 Kya, cf. Nichols 1990) is unlikely." But when Nichols's conservative estimate is based on the fact that there are 140 independent linguistic stocks in America, each at least 3,000 years old. This makes the conclusion by Wall et al. unlikely, not the other way around. If the bottleneck was indeed severe, it would've depleted the founding Native American population to such low numbers that these numbers wouldn't be able to support more than a couple of distinct languages. But then how would those languages spawn such a phenomenal linguistic diversity in only 12,500 years?

"our results are consistent with archeological estimates for the colonization of the Americas."

After the Zhirendong chin refuted all the molecular clock estimates for the departure of humans from Africa, which geneticists also claimed were compatible with fossil evidence, this new miraculous correlation between genetics and archaeology is very suspicious.

Low levels of diversity and high levels of linkage disequilibrium in the Native Americans are consistent with an entry of any antiquity provided population size has stayed low. Neanderthals seem to be lacking in diversity, too, but, by the time they went extinct, they are much older than modern humans.

"The people at Cornell's American Indian Program probably maintain that American Indians did not migrate from Siberia but were created here by one of the gods..."

True, the standard Bering Strait theory and the overkill hypothesis have been mocked - rather wittily and deservedly - by Native American intellectuals on a number of occasions. See, e.g., Vine Deloria's Red Earth, White Lies. It's true that Native American activist scholars consider the Bering Strait theory a by-product of colonialism and an artifact of American ideology whereby everybody is an immigrant in the U.S., whether 10,000 years ago or 10,000 years from now. But I don't think any Native American academic will attribute the origin of Native Americans to gods. These are tribal stories which they respect for their moral meaning - unlike the Bering Strait story - but not for their literal meaning. I listened to Scott Momaday's interview at some point and as an answer to the question where humans originated he said "I don't know." Native American intellectuals aren't afraid to say that they don't know something. Western science, on the other hand, is always under internal and external pressures to give a definitive answer regardless of the quality of the underlying data.

"the standard Bering Strait theory and the overkill hypothesis have been mocked - rather wittily and deservedly - by Native American intellectuals on a number of occasions".

I can see why many Native Americans are unwilling to give the overkill hypothesis credence but the theory fits very well with a 12,5000 year arrival. when, of if, that date is proved wrong the overkill theory may have to be discarded. but till then I'm happy to accept it.

By the way, 'overkill' is not an appropriate name. All that's required is increased predation of the young of slow-reproducing species and you have extinction.

"if, that date is proved wrong the overkill theory may have to be discarded. but till then I'm happy to accept it."

Terry, the Clovis I arrival has been refuted by Monte Verde II and Paisley Cave, at least. Monte Verde II doesn't show the lithics required for successful big game hunting. Plus in the majority of sites in North America we don't see a direct association between megafauna and human hunting.

In general, I think data from Australia, Africa and Europe indicate that it's a combination of factors, rather than a sole human-induced niche disruption, that is responsible for megafauna extinctions. More importantly, a sharp increase in population size of humans in-situ, without a transcontinental migration, can create the appearance of a deadly blitzkrieg.

I'm fine with overkill hypotheses existing, but their ability to explain facts is too poor to justify using them as a null hypothesis.

Archaeology has laid a poor foundation for open discourse with many researchers still being dead set against a deeper pre-Clovis Cultural horizon. It’s time to face up to the archaeological challenge and loosen 75 years of “convention wisdom” and get well beyond the Clovis First threshold. A brief example of the history of the earlier “just Clovis” debate should provide a background for greater dialogue not simple dismissal for even greater antiquity for Amerindians.

“At the time, Ales Hrdlicka, curator of the Smithsonian's Division of Physical Anthropology, dominated the field of anthropology. In the nineteenth century, many unsupported claims had been advanced "proving" the Indians had been in the New World for tens and even hundreds of thousands of years. But by Hrdlicka's time, a powerful reaction against such claims had developed. Hrdlicka became the leader of the skeptics, undertaking a crusade to debunk what he considered bad science. His view, based on skull morphology, was that Indians had arrived in the New World no earlier than 1,000 B.C. When any unfortunate archeologist made an assertion to the contrary, Hrdlicka reacted so vigorously that he sometimes ruined the career of his target. By 1925, the atmosphere was such that most archeologists were too intimidated to make a report. The subject of early humans in America was effectively taboo (p. 18).

The concept of an initial "settlement of the Americas" has long been set against the backdrop of the consensus paradigm: that Clovis hunters were the New Worlds first human inhabitants. This view has been in vogue for over 75 years while even this limit was difficult to establish at first, as Preston points out. Mirroring the difficulty Clovis proponents had in establishing an Ice Age presence of Mankind in the Americas are the researchers of Monte Verde, led by Tom Dillehay. The acceptance of even earlier inhabitants then the Paleoindian Clovis Culture has been gaining steam over the past century and, as the train finally arrives at the station - a little late and a little worn from the journey – its seems few are certainly ready to rejoice in the shadows of the pristine evidence substantiating Monte Verde as the first accepted mid-Pleistocene occupation. The first quarter of the last century and the reputations that were both won and lost have no less of a parallel in today's evaluation of the significance of an Amerindian Pleistocene occupation. Dillehay and his team may have won the battle of attrition but does the growing acceptance of Monte Verde II promises to redirect an interdisciplinary One World evaluation integrating a mid-Pleistocene occupation of the Americas. If we could only agree to examine MV I, as a viable occupation 33,000ybp, scientists might get beyond this checkpoint too.

"I'm fine with overkill hypotheses existing, but their ability to explain facts is too poor to justify using them as a null hypothesis".

It seems that through much of the world megafauna extinction is associated with the arrival of humans. Apart from the recent definite examples, such as Madagascar and New Zealand, there is no doubt that it goes back as far as 46,000 years in Australia. For many reason I believe America fits the scenario as well.

"More importantly, a sharp increase in population size of humans in-situ, without a transcontinental migration, can create the appearance of a deadly blitzkrieg".

I agree that over-population is always the immediate cause of the extinctions. However we know from other species that over-population usually follows initial population relatively quickly.

For example several bird species have arrived as stragglers in New Zealand since Europeans arrived, and have since become widespread. The pattern has basically been the same in each case, and so it's likely we can extrapolate to other species, including the human species.

Numbers build up slowly over several generations while the population remains confined to the region where they first entered. Then they're off. But the spread is not even. They occasionally establish populations far from their point of entry. Eventually they fill the whole region in suitable habitats.

Human expansion was almost certainly similar. Population growth in each region would be slow at first, but then after a few generations: rapid. Exponential. Rapid population growth leads to depleted resources.

Again we find examples in other species. Humans are not the only species that has caused extinction of other species. Goats virtually exterminated two plants on some islands just north of New Zealand. Just one plant of each survived. A climber and a tree. Of course they may have completely exterminated others we know nothing about because none at all survived.

The climber grows easily from cuttings and has been widely propagated. I even have one at home here. But it was doomed on the island even after goats were eliminated. The original plant does not now flower. But the cuttings do. So it survives, but only through human intervention.

The tree has also been propagated but is doomed in its original habitat. The single plant is unisexual. Luckily some cuttings have turned hermaphrodite, so many people now have it too in their garden.

The megafauna extinction in America suggests humans reached there in numbers only about 12,500 years ago. Presumably their original arrival had been several generations before that time, but is unlikely to have been more than 500-1000 years earlier. And possibly much less. The only way human prsence in America could be very much older is if the original numbers were so few that inbreeding depression prohibited population from any real expansion. It was only the later arrival of others that provided the hybrid vigour necessary for population growth.

"It seems that through much of the world megafauna extinction is associated with the arrival of humans. Apart from the recent definite examples, such as Madagascar and New Zealand, there is no doubt that it goes back as far as 46,000 years in Australia. For many reason I believe America fits the scenario as well."

Even immediate history revolts against your ideas, Terry. In the case of Madagaskar and New Zealand it's island geography and advanced technology that enabled a dominants incoming species to deplete local megafauna, not sheer population growth/colonization. You can conduct an experiment by locking two humans with spears and guns and a few large animals into a cage - and you'll see extinction. In the case of diverse non-island environments, American bison survived both Pleistocene extinctions and the European colonization of North America. It was placed on the verge of extinction by firearms used for entertainment, not by human occupation per se and human needs to survive. Later it was salvaged by deliberate human efforts and now it's being bred even outside of North America.

In the Lower Pleistocene, Africa first suffered local megafauna extinctions, although there was no migration of hominids into Africa. Then in the Late Stone Age it retained some of its megafauna, although modern humans armed with new tools expanded all across the continent from an original East African center of dispersal. Ancient humans and ancient megafauna didn't care if expansion happened from a single area on a continent or from a different continent. So, the result should be the same, whether modern humans colonized Africa from another continent or from a region within Africa. The fact that giraffes still walk around proves that humans are not responsible for Pleistocene extinctions.

There's no causal relationship between the presence of humans/hominids and the extinction of megafauna. And you can't divine human presence on the basis of megafauna extinctions. Humans and hominids do hunt and they do grow in size, so they may become a contributing factor but it's a combination of climate change, geography and niche competition that leads to extinctions.

"The megafauna extinction in America suggests humans reached there in numbers only about 12,500 years ago. Presumably their original arrival had been several generations before that time, but is unlikely to have been more than 500-1000 years earlier. And possibly much less. The only way human prsence in America could be very much older is if the original numbers were so few that inbreeding depression prohibited population from any real expansion."

You're approaching the issue from a wrong perspective. If you want to argue for a recent colonization of the Americas, you have to find a Clovis antecedent in Siberia. It hasn't been found, so Paleoindians are covered by the "presumption of innocence," unless shown otherwise.Plus Clovis technologies flourished for only a short period of time. Native American population numbers are the lowest continental numbers, so this is a proven fact. Their levels of homozygosity are the highest worldwide, so, again, nothing strange or new here. Modern humans originated from a small founding population, which suggests that Amerindians preserved this ancient population structure, while other populations, especially Africans deviated from it.

"The fact that giraffes still walk around proves that humans are not responsible for Pleistocene extinctions'.

No it doesn't. All it proves is 'that humans are not responsible for Pleistocene extinctions' in Africa. Giraffes outside Africa certainly dissappeared at the end of the Pleistocene, especially the antlered giraffe, sivatherium:

"The fossil record of the Giraffidae begins in Africa during the Miocene, extending to the present on this continent. Giraffes also ranged widely in Eurasia from the middle Miocene to the Pleistocene".

"There's no causal relationship between the presence of humans/hominids and the extinction of megafauna".

Yes there is. Whenever humans have arrived in a region large mammals with slow reproductive rates have become extinct. The fact many such mammals survive in Africa is presumably a product of their long co-evolution with humans in that continent.

"In the case of diverse non-island environments, American bison survived both Pleistocene extinctions and the European colonization of North America".

Bison breed when just two years old, and have one calf a year. They could hardly be described as 'slow reproducing'. What about American mammoths, ground sloths, giant armadillo, horses, camels, etc.? All suddenly extinct around 12,000 years ago.

"In the Lower Pleistocene, Africa first suffered local megafauna extinctions, although there was no migration of hominids into Africa".

Of course 'there was no migration of hominids into Africa'. They were already there.

"And you can't divine human presence on the basis of megafauna extinctions".

Basically you can. Their presence coincides remarkably well.

"they may become a contributing factor but it's a combination of climate change, geography and niche competition that leads to extinctions".

The book "Australia's Mammal Extinctions" by Chris Johnson should be required reading. He examines all the excuses you've offered for the extinctions and shows that just one other one stands up to scrutiny: humans did it. Some links:

"one universal prediction, which applied in all scenarios in which the empirical distribution was correctly predicted, was for the extinctions to be rapid following human arrival and for surviving fauna to be suppressed below their pre-‘blitzkrieg’ densities. In sum, human colonization in the late Pleistocene almost certainly triggered a ‘blitzkrieg’ of the ‘megafauna’, but the operational details remain elusive".

"The book "Australia's Mammal Extinctions" by Chris Johnson should be required reading."

Terry, there're hundreds of publications about extinctions. You picked one that supports your view. This proves nothing. C. Johnson is just another guy with no common sense. Ask your friend Maju for the literature that challenges the overkill hypothesis and brings up a variety of factors to explain the extinctions.

"The fact many such mammals survive in Africa is presumably a product of their long co-evolution with humans in that continent."

This is just absurd. If several increasingly advanced hominids originated in Africa and dispersed across Africa and the rest of the world, then they had many more opportunities to kill off African megafauna than the megafauna on other continents. Humans hunt megafauna all over the globe, Pygmies hunt elephants with spears, Homo erectus hunted big game. Supposedly, we find advanced hunting technology such as bows and arrows and pressure flakes in Middle Stone Age contexts in Africa. Plenty of observers saw Pygmies stick a spear into an elephant's underbelly. The spear is a spear in Africa, in Australia and in America. Elephants are slow reproducing animals. Plus, Africa and Europe are known to have harbored large hominid populations (unlike Asia, Austrtalia and America where hominid/human populations were sparse and small), which would've been directly conducive to megafauna extinctions.

There's no such thing as "long-term peaceful co-existence" between populous and advanced hunters and the slow-reproducing prey. But despite millions of years of hunting African megafauna hominids demonstrably didn't make its megafauna go extinct. It means humans are not the sole cause of megafauna extinction in Africa or elsewhere. Case dismissed.

"In the Lower Pleistocene, Africa first suffered local megafauna extinctions, although there was no migration of hominids into Africa".

Of course 'there was no migration of hominids into Africa'. They were already there."

Doesn't that directly contradict your idea that transcontinental migrations lead to extinctions, hence you can divine the timing of human emergence in a continent such as Australia or America by the time megafauna went extinct there?

"Basically you can. Their presence coincides remarkably well."

Here we go. Coincidence is not causality. And there's nothing remarkable about in-situ expanding human populations, geographic constraints of island environments and climate change. They all worked together. BTW, judging by the presence of mtDNA M23 in the Mikea of Madagascar, it's likely that Austronesians were not the first humans to colonize that island. Hence, even the temporal coincidence between extinctions and human arrivals may not be there.

"Bison breed when just two years old, and have one calf a year. They could hardly be described as 'slow reproducing'. What about American mammoths, ground sloths, giant armadillo, horses, camels, etc.? All suddenly extinct around 12,000 years ago."

Bison is just one of the case studies that proves that humans are not the sole cause of megafauna extinction in the Pleistocene. A combination of factors such as climate change, geography, niche competition, including in-situ expanding human populations in the New World led to the extinction of many megafauna species. Bison co-existed with humans all along and was hunted pretty extensively but he found a geographic niche on the Great Plains where it survived.On the other hand, woolly mammoths in Siberia were replaced by their own relatives coming from northern North America. See Debruyne et al. (2008). "Out of America: Ancient DNA evidence for a New World origin of Late Quaternary woolly mammoths". Current Biology 18 (17): 1320–1326.

"BTW, judging by the presence of mtDNA M23 in the Mikea of Madagascar, it's likely that Austronesians were not the first humans to colonize that island. Hence, even the temporal coincidence between extinctions and human arrivals may not be there".

How does M32's presence show that the Austronesians were not first to Madagascar? It is virtually certain that M23 arrived with the Austronesians, the first people to reach Madagascar. M23 is found in Laos and is a clade of M23'75. M75 is also SE Asian. So the evidence of human arrival leading to simultaneous extinction holds up very well for that island.

"If several increasingly advanced hominids originated in Africa and dispersed across Africa and the rest of the world, then they had many more opportunities to kill off African megafauna than the megafauna on other continents".

Just yesterday you provided evidence that they did so:

"In the Lower Pleistocene, Africa first suffered local megafauna extinctions, although there was no migration of hominids into Africa".

So there you have it. Africans killed their megafauna early on in the piece. The surviving megafauna adapted to human presence.

"A combination of factors such as climate change, geography, niche competition, including in-situ New World led to the extinction of expanding human populations in the many megafauna species".

Just think about it for a moment. Just one of those excuses actually adds up. The others have huge problems.

"On the other hand, woolly mammoths in Siberia were replaced by their own relatives coming from northern North America".

But that was long before humans had reached either region. And the mammoths that entered Siberia dissappeared very soon after people reached there. Same with America.

"Ask your friend Maju for the literature that challenges the overkill hypothesis and brings up a variety of factors to explain the extinctions".

He has provided a mountain of completely unconvincing evidence. So, like him, you believe that by an amazing coincidence a whole suite of mammoth species died out, for completely different reasons in each case, at roughly the same time that humans arrived in each region. This in spite of there being one common factor at the time of extinction of all those species. Surely for both of you this belief is simply a desperate attempt to avoid facing an obviously unpalatable fact: Homo sapiens is an environmentally destructive species. And Maju has still not satisfactorily explained how the mammoths on the islands off California suffered extinction through human influence yet the mammoth extinction on the mainland, at precisely the same time, was caused by something other than human presence.

"M23 is found in Laos and is a clade of M23'75. M75 is also SE Asian."

Good to know. I elaborated on this fact http://blogs.discovermagazine.com/gnxp/2011/03/out-of-south-africa/

"The surviving megafauna adapted to human presence."

Terry, how in the world can megafauna (think of giraffes, for a second) "adapt" to human hunting? You anthropomorphize megafauna: Australian and American megafauna was "naive", while African megafauna was "savvy." But the truth is it's humans who, indeed, are behaviorally very malleable. The fact that Pleistocene megafuna largely survived in Africa may mean that Africa was colonized by modern humans no earlier than 50K years ago, and since it was a new continent for them they behaved tentatively and adapted to the megafauna, thus sparing it.

All these facts refute the anthropogenic theory of extinctions. It's the pattern of survival of megafauna may have an anthropogenic origin, not the pattern of extinction.

"how the mammoths on the islands off California suffered extinction through human influence yet the mammoth extinction on the mainland, at precisely the same time, was caused by something other than human presence."

Island geography is a special case. Plus mind you nobody has reported direct archaeological association between the remains of megafauna on these islands and human hunting.

"And the mammoths that entered Siberia dissappeared very soon after people reached there."

And the mammoths in Estonia survived until 8,000 BC, long after humans had re-colonized northern Europe.

"Just one of those excuses actually adds up. The others have huge problems."

Exactly the opposite. In America and Australia, with their sparse foraging and scavenging populations, the majority of species of megafauna went extinct; in Africa and Europe, the most populous regions since Lower Pleistocene, very few species of big game disappeared: 7 of 23 in Europe and 2 of 44 in Sub-Saharan Africa. In the New World, the giant sloth went extinct, although it was never hunted. Even a few tree species went extinct. Did Paleoindians hunt them, too?

Perhaps. But the time of mammoth extinction on those islands coincides remarkably with the mammoth extinction on the nearby mainland. So in what way are those islands 'a special case'?

"Plus mind you nobody has reported direct archaeological association between the remains of megafauna on these islands and human hunting".

So it's a complete coincidence that mammoths died out very soon after humans arrived there? Besides which I pointed out that just a very small increase in predation of slow-reproducing animals is enough to cause extinction.

"In the New World, the giant sloth went extinct, although it was never hunted".

How do you know that?

"And the mammoths in Estonia survived until 8,000 BC, long after humans had re-colonized northern Europe".

"But the time of mammoth extinction on those islands coincides remarkably with the mammoth extinction on the nearby mainland. So in what way are those islands 'a special case'?"

Humans do hunt, so do other predators, climate does change, mammoths did go extinct, they could go extinct through a variety of ways, on islands the human factor may have played a larger role than on mainland. It's very simple. The best way to approach Pleistocene extinctions is through the so-called "individual species" paradigm developed by American ecologists. See the works by Elin Whitney Smith, among others. The only reason why you believe humans are responsible for extinctions is because you take a very abstract, decontextualized view of the matter. And then you fit in all exceptions, as they come in, using a circular argument.

"Are you sure they didn't develop it simply to avoid facing the obvious?"

If something that happened 12,000 years ago is "obvious" to my contemporary, then I will have to say that my contemporary is most likely wrong. The idea is that every species has it's own history of emergence, survival and extinction. One single anthropogenic factor is just too simplistic, especially when we still know very little about those extinct species.

"Yes. because the extinction of the megafauna changed the ecology."

You attribute to foragers the destructive powers of biblical God. Do you know that the bison actually split into 2 distinct species as a result of the actions of your "angry red man"?

"But there is just one common factor in all the extinctions."

There's no "one common factor in this extinctions." Hunter-gatherers hunt. It's a fact. They hunt big and small animals. That's why they are called "hunter-gatherers." But there's no evidence that hunter-gatherers hunt the source of their livelihood to extinction. And there's no evidence that the Late Pleistocene hunters in the New World came from Asia, rather than increased in size in-situ and developed more powerful hunting tools.

"How does that tell us that humans didn't hunt them?"

I thought you knew "how": because none of the remains of ground sloth recovered to date are associated with human hunting (butchering sites, projectile points embedded in bones, cut marks, etc). Unless you believe humans strangled them, it stands to reason that ground sloth didn't need human intervention to go extinct. But then the dung analysis suggested that diet may have been the reason.

"Question: When did humans arrive in Estonia? Answer: Sometime between 8,500-11,000 BC. When the climate changed".

Next question: When did mammoths become extinct in Estonia? Answer (quoting you): the mammoths in Estonia survived until 8,000 BC"

Surprise, surprise. Especially considering that mammoths had survive innumerable similar changes of climate before that time. Are you in the pay of those advocating carbon tax?

"The idea is that every species has it's own history of emergence, survival and extinction".

Yes, but that 'history of emergence, survival and extinction' does not take place in a vacuum. The study of ecology is actually the study of the inter-action of species. So to examine each species separately seems to me to be a deliberate attempt to obscure the fact that many different species became extinct at the same time. You can concoct a theory that doesn't include humans to account for a single species' dissappearance, but it is much more difficult to do so if you consider the extinctions together.

"One single anthropogenic factor is just too simplistic, especially when we still know very little about those extinct species".

We know a great deal about when each of them became extinct. The 'single anthropogenic factor' of human arrival is the one factor they all have in common.

That is completely irelevant. I have tied top point out to you many times that hunting pressure of slow-reproducing species does not have to be extreme to lead inevitably to extinction. Make some small effort to find some papers on the subject, please.

"You attribute to foragers the destructive powers of biblical God".

And you seem to believe that God was looking after the megafauna and making sure that human hunting did not interupt their existence in any way.

"But there's no evidence that hunter-gatherers hunt the source of their livelihood to extinction".

There is plenty of evidence that humans have done so in historic times. And even during recent pre-history.

Sounds suspiciously as though they did need human intervention to go extinct. They'd survived quite well for a very long time before humans arrived. And survived massive climate change.

"But then the dung analysis suggested that diet may have been the reason".

That change in diet was presumably a result of change of vegetation. But the change in vegetation was itself almost certainly the result of decrease in the megafauna numbers, rather than being simply associated with climate change.

"And there's no evidence that the Late Pleistocene hunters in the New World came from Asia, rather than increased in size in-situ and developed more powerful hunting tools".

And that sums up in one sentence why you are so opposed to accepting humans were responsible for megafauna extinction. It contradicts any 'out of America' scenario.

"Surprise, surprise. Especially considering that mammoths had survive innumerable similar changes of climate before that time."

Climate change explains both the migration of humans to Estonia and the disappearance of mammoths. Humans did hunt them not doubt, but you haven't provided any evidence that human hunting caused their extinction. Past climate changes had a different affect on the megafauna.

"The study of ecology is actually the study of the inter-action of species."

Sure. The individual species paradigm explores the interaction between an individual species and its environment over the period of its existence. Humans are part of it, no doubt, so are other species.

"The 'single anthropogenic factor' of human arrival is the one factor they all have in common."

Only in your mind's eye, Terry. Africa and Europe were occupied by humans and hominids the longest and hominid numbers were there the greatest, but these are precisely the areas where megafauna ended up relatively spared. This simple fact kills the anthropogenic factor theory.

"And you seem to believe that God was looking after the megafauna and making sure that human hunting did not interupt their existence in any way."

Not at all. Sometimes and in some places humans contributed to their extinctions, in other places they apparently spared them. But humans are not the sole, straightforward factor.

"I have tied top point out to you many times that hunting pressure of slow-reproducing species does not have to be extreme to lead inevitably to extinction."

Then Neanderthals and African archaics would have killed off the slow reproducing megafauna before modern humans. But, again, they didn't.

"And that sums up in one sentence why you are so opposed to accepting humans were responsible for megafauna extinction. It contradicts any 'out of America' scenario."

The current theories of the peopling of the Americas can't withstand a close scrutiny because they are steeped in myths like "Pleistocene overkill." In any case, even the overkill theory can't hurt out of America because the "single anthropogenic factor" idea has to admit that humans and megafauna can co-exist peacefully, as the African record demonstrates. Pygmies continue to hunt elephants without the latter going extinct. So, this could've happened in the New World in pre-Clovis times. Then the big projectile points were invented, populations grew and megafauna became as easier prey and a roadblock to better niches.

Here's a recent article on hyenas in Europe. Climate change was the major factor in their extinction.

Were the Late Pleistocene climatic changes responsible for the disappearance of the European spotted hyena populations? Hindcasting a species geographic distribution across time, by Sara Varela et al. 2010.

"Climatic conditions in Southern Europe during the Late Pleistocene remained within the spotted hyena climatic tolerance. Hence, climate changes could have directly affected the Northern distribution of the species during the last glaciations. However, climate change alone is not sufficient to have caused the disappearance of the spotted hyena populations in Southern Europe. That is, other factors, such as prey abundance or human ecological impacts, in addition to climatic change, are needed to completely account for extinction of the European spotted hyena".

So when you pose the question, 'Were the Late Pleistocene climatic changes responsible for the disappearance of the European spotted hyena populations?' the answer is a resounding: NO.

"Climate change explains both the migration of humans to Estonia and the disappearance of mammoths. Humans did hunt them not doubt, but you haven't provided any evidence that human hunting caused their extinction. Past climate changes had a different affect on the megafauna".

Why would that be so? To quote you,'you haven't provided any evidence'. Human presence is the only different factor.

"Africa and Europe were occupied by humans and hominids the longest"

True. But is appears as though effective big animal hunting did not develop until something like 50,000 years ago, presumably through the development of new technolgy or tecniques. And that is evidence for a back-movement into Africa at some time. Perhaps Y-hap E fits.

"Then Neanderthals and African archaics would have killed off the slow reproducing megafauna before modern humans. But, again, they didn't".

"So when you pose the question, 'Were the Late Pleistocene climatic changes responsible for the disappearance of the European spotted hyena populations?' the answer is a resounding: NO."

I've been always saying, Terry, it's a combination of various factors, including climate change, human hunting, niche competition with other species, and who knows what else that caused extinction and dwarfing of the megafauna. But it's climate change that provided the first and continuing impetus. This made humans compete with other carnivores for niches, and the latter in turn drove herbivores to extinction. So, the large herbivores suffered from the compounded impact of changing climate, human and animal carnivore hunting.

"True. But is appears as though effective big animal hunting did not develop until something like 50,000 years ago, presumably through the development of new technolgy or tecniques. And that is evidence for a back-movement into Africa at some time. Perhaps Y-hap E fits."

This is an interesting idea, Terry. Finally, you're shifting gears from advocacy to analysis. Although apparently bows and arrows and Clovis/Solutrean-looking projectile points appear during the Middle Stone Age in Africa. Lower Pleistocene in Africa also witnessed megafauna extinction, which again suggests, if hominid hunting was responsible for it, that a trans-continental hominid migration is not a necessary condition.

"Presumably because they hadn't developed the required tecniques."

Australian aborigines at 50-40,000 years didn't have an Upper Paleolithic hunting toolkit either. If, according to you, they caused megafauna extinctions in Australia, then Neanderthals should've caused it in Europe. Chris Johnson at least acknowledges that the lack of advanced hunting tools in the earliest Australian archaeological record constitutes a problem for the overkill hypothesis.

In North America, indigenous hunter-gatherers practiced collective caribou (in Subarctic) and buffalo (on the Great Plains and in the Great Basin) hunting for millennia. In the 18th century indigenous buffalo hunters even acquired horses to optimize their hunting technique. Neither the caribou, nor the buffalo went extinct, though, as a result of the indigenous effort. Only European leisure hunting, using firearms, led to the extinction of the bison in the Great Basin (by 1840) and placed the bison on the verge of extinction on the Great Plains. So, only after human technology and population numbers cross a certain threshold that they can exert a systematic negative impact on ecology and approximate climate change in its wide-ranging and lasting consequences.

"True. But is appears as though effective big animal hunting did not develop until something like 50,000 years ago, presumably through the development of new technolgy or tecniques. And that is evidence for a back-movement into Africa at some time. Perhaps Y-hap E fits."

One more thought on that. If Y-DNA E comes from a back-migration to Africa and corresponds to the development of microlithic industries, population growth (for which there's archaeological evidence) and increased big game hunting, then Y-DNA hgs A and B (assuming they were present in Africa prior to the migration of hg E and didn't come to Africa as a parallel coastal migration) represent a human population with a different system of adaptation, which didn't exert much pressure on the environment. Perhaps, the original carriers of Y-DNA hgs A and B scavenged and fished rather than hunted.

In any case, judging by the pattern of African extinctions, without a climate change, even the microlith-equipped, expanding E people couldn't do much damage to the megafauna.

You may benefit from reading Binford's Faunal remains from Klasies River Mouth (1984). In it, Binford aims at evaluating the relative roles of scavenging versus hunting in the subsistence tactics of ancient hominids, in this case the populations of the Tzitzikama Coast of South Africa in the Late Pleistocene. He questioned and contradicted the conclusions of Richard Klein and other believers in the "man the hunter" and "Pleistocene overkill" myths and considers these people of the South African Middle Stone Age not efficient hunters of large game but in a transitional stage between a virtual reliance on scavenging and the development of elementary hunting techniques that at least allowed them to take small antelopes.

All of this means that modern humans are capable of two adaptation strategies: invasive and non-invasive. Hence, from the timing of Pleistocene extinctions, you absolutely can NOT divine the physical presence of ancient humans, but only the presence of a particular type of adaptation. Going back to the New World, there must have been a human population that significantly pre-dated the population of big game hunters that participated (with climate change) in bringing Pleistocene extinctions on the local megafauna.

"It is clear that the dramatic environmental changes occurring throughout the Pleistocene detrimentally affected the abundance and distribution of megafauna in the region. Conversely, there is very little evidence to suggest that Pleistocene Southeast Asians negatively affected the megafauna until the Holocene. Direct, unequivocal evidence of human hunting of megafauna in Southeast Asia is non-existent for either Homo erectus or archaic Homo sapiens, and it appears that hunting of megafauna by modern Homo sapiens did not become unsustainable until the past 2000-3000 years (Corlett, 2007). Furthermore, the Pleistocene Southeast Asian toolkit appears to have been unsuited to the hunting of large game. Pleistocene stone tools from Southeast Asia consisted largely of choppers, and did not achieve the sophistication of the European toolkit until the Late Pleistocene/Early Holocene (Reynolds, 1990; Corvinus, 2004). Habitat alteration by humans also appears to have been negligible until the Holocene, and human-induced firing of the landscape appears to have become important only in the past 1400 years (Anshari et al., 2001). The negative ecological effects of humans in region have, however, escalated since the beginning of the Holocene." (Louys, "Quaternary extinctions of Southeast Asia’s megafauna," 2007).

By extension, this likely means that humans who colonized Australia (ultimately, from SEA) couldn't have been responsible for megafauna extinction there. The temporal association between last megafauna and first humans in Australia is, therefore, likely a coincidence. It's possible that humans were just the last drop in the long process of megafauna deterioration in Australia caused by increasing aridity.

"If Y-DNA E comes from a back-migration to Africa and corresponds to the development of microlithic industries, population growth (for which there's archaeological evidence) and increased big game hunting, then Y-DNA hgs A and B (assuming they were present in Africa prior to the migration of hg E and didn't come to Africa as a parallel coastal migration) represent a human population with a different system of adaptation, which didn't exert much pressure on the environment. Perhaps, the original carriers of Y-DNA hgs A and B scavenged and fished rather than hunted".

That is my guess.

"the Pleistocene Southeast Asian toolkit appears to have been unsuited to the hunting of large game".

That may be relevant.

"It's possible that humans were just the last drop in the long process of megafauna deterioration in Australia caused by increasing aridity".

There is absolutely no evidence that megafauna numbers were diminishing in Australia at all before they suddenly died out at the generally accepted time of human arrival.

"The temporal association between last megafauna and first humans in Australia is, therefore, likely a coincidence".

Coincidence? I don't thinlk that is likely.

"By extension, this likely means that humans who colonized Australia (ultimately, from SEA) couldn't have been responsible for megafauna extinction there".

It is surely becoming more and more likely that the megafauna extinction in Australia was caused purely and simply by humans.

"You may benefit from reading Binford's Faunal remains from Klasies River Mouth (1984)".

And you would benefit from reading the recent book "Australia's Mammal Extinctions" by Chris Johnson. Concerning SE Asia:

"It is clear that the dramatic environmental changes occurring throughout the Pleistocene detrimentally affected the abundance and distribution of megafauna in the region".

I was not aare of any species extinction in SE Asia during the Pleistocene. What species is the author refering to?

"Conversely, there is very little evidence to suggest that Pleistocene Southeast Asians negatively affected the megafauna until the Holocene".

If there were extinctions in the Pleistocene on what grounds can the author then claim that humans were not responsible for them? And surely the extinctions in the Holocene coincide completely with the arrival of Neolithic Humans. The implication of lack of extinction before then may just indicate the human population was very sparsely distributed until then. In fact I suspect the mountains were probably uninhabited until the Neolithic.

And another thing. You and Maju are very much alike. I've pointed out to him that the pandas' range contracted as the humans' range expanded. Pandas survive only in regions humans have just recently entered, and are heading rapidly to extinction in those regions. He argues I have no dates for either the panda range contraction or the human range expansion. But I'd bet any amount of money that dates for the two events can be ascertained they will coincide.

Some time back you claimed:

"It's one of your favorite circular argument".

The sequence went like this:

1) Humans may have had a hand in mammoth extinction. 2) Mammoths in Estonia survived until 8,000 BC. 3) That may have been because humans hadn't reached Estonia by then. 4) Humans arrived in Estonia sometime between 8,500-11,000 BC. 5) Conclusion: Humans almost certainly had a hand in that extinction.

"it's a combination of various factors, including climate change, human hunting, niche competition with other species"

How could climate change and niche competition lead to hyena extinction when they had survived both many times before?

"Lower Pleistocene in Africa also witnessed megafauna extinction, which again suggests, if hominid hunting was responsible for it, that a trans-continental hominid migration is not a necessary condition".

Quite. It actually shows that Africans have been quite capable of leading other species to extinction for quite some time. But I'm not blaming them. The arrival of any new species upsets any 'balance' that may exist.

"Chris Johnson at least acknowledges that the lack of advanced hunting tools in the earliest Australian archaeological record constitutes a problem for the overkill hypothesis".

But he then sets about explaining exactly how it was possible, even extremely likely.

"Neither the caribou, nor the buffalo went extinct, though, as a result of the indigenous effort".

Of course not. They ar not 'slow-reproducing' animals. The females breed at two years and produce one offspring a year.

"So, only after human technology and population numbers cross a certain threshold that they can exert a systematic negative impact on ecology and approximate climate change in its wide-ranging and lasting consequences".

But for slow-reproducing animals that threshold of human population numbers is much lower. And if humans behaved like most other species their numbers would increase exponentially once they entered a previously uninhabited region. Neanderthal population may have been kept in check by predators, or genetic diseases resulting from inbreeding.

"There is absolutely no evidence that megafauna numbers were diminishing in Australia at all before they suddenly died out at the generally accepted time of human arrival."

There's no "generally accepted date" for human arrival in Australia. If megafauna is Australia went extinct at 45,000, humans may not have got to Australia for another 5,000 years. Or they may have arrived there by 60,000 years.

"Coincidence? I don't thinlk that is likely."

Unlikely is not impossible, plus how can you measure likelihood here? Coincidence is perfectly fine with me. Terry you still don't understand how science works: you have to provide evidence (cut marks, embedded projectile points, etc., plus a quantitative analysis of species population in proportion with the number of sites attesting to human hunting, etc.), not an abstract "likelihood."

"And you would benefit from reading the recent book "Australia's Mammal Extinctions" by Chris Johnson."

I read it.

"I was not aare of any species extinction in SE Asia during the Pleistocene. What species is the author refering to?"

I referenced the paper. Now go online and locate it. Then read it.

"If there were extinctions in the Pleistocene on what grounds can the author then claim that humans were not responsible for them?"

That's not how it works, Terry. YOU have to provide the positive evidence that human hunting made megafauna go extinct. If there was evidence for that in the archaeological record, then the author would've reported it. But there's none.

"The implication of lack of extinction before then may just indicate the human population was very sparsely distributed until then."

Finally, Terry, you are learning from the data, not from your own biases.

"The sequence went like this..."

I'm not going to address your continuing attempt to convert coincidence into causality. Show me the overkill sites in Estonia, show me the correlation curve between the number of overkill sites and the decreasing population of mammoths, and we'll talk. For now, "humans almost certainly had a hand in that extinction" is nonsense. Humans are hunters and they hunted mammoths. Unsustainable hunting is a whole another issue. This needs to be proven.

"How could climate change and niche competition lead to hyena extinction when they had survived both many times before?"

You are asking medieval questions, Terry. To this I'll answer with another question: how could primitive foragers kill of over a hundred of genera of megafauna?

"They ar not 'slow-reproducing' animals. The females breed at two years and produce one offspring a year."

More than 30 genera of megafauna went extinct in North America. That's way more offspring per year than caribou and bison can deliver. Foragers are "slow-reproducing," too, hence they didn't need that much food.

"And if humans behaved like most other species their numbers would increase exponentially once they entered a previously uninhabited region."

That's what we see in the African and European archaeological record.

"Neanderthal population may have been kept in check by predators, or genetic diseases resulting from inbreeding."

Terry, another good paper to read is this one: Late Quaternary Extinctions: State of the Debate, byPaul L. Koch and Anthony D. Barnosky // Annual Review of Ecological and Evolutionary Systems 2006. 37:215–50. It gives an overview of all possible angles on the problem, without advocating for a conspiracy theory. Look for it online or go to the library.

"Slow-breeding animals also were hard hit, regardless of size. This unusual extinction of large and slow-breeding animals provides some of the strongest support for a human contribution to their extinction and is consistent with various human hunting models, but it is difficult to explain by models relying solely on environmental change".

Sounds to me as though they agree humans were responsible. And they certainly do not agree with you when you say:

"You are asking medieval questions, Terry".

Climate change cannot have been responsible for megafauna extinction. They do concede that:

"the timing and geography of extinction might have been different and the worldwide magnitude less, had not climatic change coincided with human impacts in many places".

But climatic change certainly does not coincide with the extinctions in Australia.

"There's no 'generally accepted date' for human arrival in Australia".

I disagree. Around 50,000 years is fairly generally accepted by most scientists in Australia. A very few claim older dates, but these are considered unlikely by most.

"That's what we see in the African and European archaeological record".

And in Australia and America.

"This would be the case for Amerindians and Australian aborigines".

No it wouldn't. The population expansion shows they were not subject to any such level of predation.

"show me the correlation curve between the number of overkill sites and the decreasing population of mammoths"

There certainly seems to be a 'correlation curve' between the number of humans and the decreasing population of mammoths.

"how could primitive foragers kill of over a hundred of genera of megafauna?"

Easily.

"Humans are hunters and they hunted mammoths".

But just a minute ago you wrote:

"Terry you still don't understand how science works: you have to provide evidence (cut marks, embedded projectile points, etc., plus a quantitative analysis of species population in proportion with the number of sites attesting to human hunting, etc.)"

So you do accept that humans hunted mammoths.

"YOU have to provide the positive evidence that human hunting made megafauna go extinct".

And that is absolutely impossible to find. You would have to be able to prove that the last mammoth had been killed by humans. That is why you are able to claim the 'benefit of the doubt'.

How about this one: www.langkau.my/wp-content/uploads/2010/04/Louys-20072.pdf

"Only because it allows you to believe what you want to believe."

There was no climate change in Africa, and the megafauna survived there. There was a climate change in Southeast Asia (sea level, etc.) and the megafauna went extinct there. The toolkit of the first Australians or SEAsians wasn't more advanced than that of Neanderthals. Neanderthals co-existed with the megafauna for hundreds of thousands of years. Human populations were quite large in Africa and Europe - the two regions the least affected by the extinctions. Human populations in America and Australia were very sparse - and continued to be in the historical period - but the megafauna went extinct there. Technologically, bows and arrows and Solutrean/Clovis-type projectile points appear first in the African Middle Stone Age, but these advanced technologies didn't yield any extinctions. Clovis projectile points are of Middle Paleolithic type flake-biface, not attested in Siberia, how could they represent a migration of Siberian hunters into the New World bringing extinction to the megafauna?

"Slow-breeding animals also were hard hit, regardless of size. This unusual extinction of large and slow-breeding animals provides some of the strongest support for a human contribution to their extinction and is consistent with various human hunting models, but it is difficult to explain by models relying solely on environmental change".

Sounds to me as though they agree humans were responsible.."

Terry, you've been advocating the anthropogenic factor as the sole cause of Pleistocene extinctions. I believe that humans were a contributing factor, next to climate, geography, etc. The paper and the abstract support my balanced and data-driven position, not your extreme and biased one. Also, although the authors claim that there's a pattern pointing to humans as a cause whereby only large and slow-reproducing animals went extinct, it's misleading. Human foragers are large and slow-reproducing animals themselves and they didn't need that much meat to maintain their numbers. Also, although size and reproduction rate do correlate, slow-reproducing animals died out regardless of size.

"So you do accept that humans hunted mammoths."

This is ridiculous, Terry. Humans hunted mammoths, Neanderthals hunted mammoths, wolves and saber-tooth cats hunted mammoths. Pygmies continue to hunt elephants. With no extinctions to follow. We should be talking about unsustainable hunting only.

"But climatic change certainly does not coincide with the extinctions in Australia."

I'm not 100% sure about that. In any case, while the climate explanation has its challenges in Australia, so does the anthropogenic one: early Australians didn't have the toolkit nor the dogs to execute the blitzkrieg. Plus archaeological evidence of the association between human hunting and megafauna is very sparse in Australia. We should exclude habitat alteration through fires, too, per recent research. One curious aspect of Australian Pleistocene fauna is the complete absence of predators prior to the arrival of humans. Maybe the megafauna was slowly deteriorating in the absence of a need for struggle for survival.

""That's what we see in the African and European archaeological record".

And in Australia and America."

Yes, to a certain extent, but if we believe the out of Africa story humans colonized the globe through a series of bottlenecks, whereby only a subset of the source population entered the new areas such as America and Australia. But that should mean that the pressure on the megafauna must have been greater in the source areas than in the colonized areas. But it's precisely in Africa that the megafauna survived the most. From my perspective, Australia was colonized by humans, America, Europe and Siberia experienced a population growth at the end of the Ice Age as new territories became available for occupation. But contrary to a common belief the pattern of Pleistocene extinctions is in stark contradiction with the serial bottleneck vision of human dispersals out of Africa. If they were well correlated, then we would've seen 1) massive extinctions in Africa between 200-50K and thereafter as populations of modern humans evolved and expanded throughout Africa from a single location; 2) a similar to Africa level of extinction in Europe after 50K; 3) restricted extinctions in Australia after 50K; 4) restricted extinctions in the New World after 12K.

The pattern of extinctions is in contradiction with the out of Africa model. The nature of the hunting toolkit in Africa and Europe (well-developed, well-differentiated) vs. SEAsia, Australia and pre-Clovis America (underdeveloped) is in contradiction with the single anthropogenic factor explanation of extinctions.

I am a person derived from both Indo-European and Amerind branches of humanity. Opinion will not stand against empirical evidence. I am y=R1b and mtDNA=H, from my dad & mom; but my dad is possible mtDNA=B, since my g-ma was 1/8th Amerind. Looks to me like an Asian origin has become clear, from DNA analysis, for Amerinds. I agree that the 'mass extinction' must be seen as taking rough 3000 years.

"Terry, you've been advocating the anthropogenic factor as the sole cause of Pleistocene extinctions. I believe that humans were a contributing factor, next to climate, geography, etc. The paper and the abstract support my balanced and data-driven position, not your extreme and biased one".

'Among late-surviving mastodons he has studied, Dan is finding examples of females losing calves (where one pregnancy is immediately followed by another, rather than by two years of lactation) and of males going into musth early (just as young bull elephants do in Africa, when mature males are poached out). Dan had also found examples of mammoths dying in the autumn, a time of year when they should have been in peak condition. Autumn deaths argued for an extrinsic cause of death. For Dan, all this could be pinned on one such cause: overhunting by humans".

"Far from rampaging across the continent, killing every large mammal in sight, it seems ancient hunters may have had a more subtle, but no less terminal impact. Over thousands of years, the level of hunting was just enough to be unsustainable for these huge, slow-breeding behemoths of the ice age".

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